Linear stability analysis of chemical mechanism, Listanalchem: A tool for the search of spontaneous mirror symmetry breaking.

Homochirality, the phenomenon by which one of two virtually identical (non-superimposable mirror images) compounds is favored over the other in the chemistry of life, has been regarded as a requisite for the emergence of all living things on earth. Spontaneous mirror symmetry breaking has been proposed to produce the imbalance. Under this framework, Frank presented, in his foundational article "On spontaneous asymmetric synthesis", a simple chemical reaction network that displays spontaneous symmetry breaking for a specific set of reaction rates. Research has since focused on finding more complex and plausible models, each one with its advantages and disadvantages. Nevertheless, finding reaction rate values that make a model exhibit spontaneous symmetry breaking is a complex task, even for specially crafted models. LInear STability ANALysis of CHEmical Mechanism, Listanalchem, is a method and software for the search for appropriate reaction rates. It includes four different algorithms inspired by the analysis of Frank's network. Two classical algorithms are also included in Listanalchem: the Trace-Determinant plane and the Stoichiometric Network Analysis by Bruce Clarke. Listanalchem reads a chemical reaction network from plain text and runs one or more of the available algorithms according to the user selection. Listanalchem is tested and verified by studying classical, modified, and recent models proposed to explain the origin of biological homochirality.•Listanalchem allows a fast and reliable search for instability behavior in chemical mechanisms that pretend to explain spontaneous mirror symmetry breaking.•Listanalchem contains several model examples, including the most cited in the related literature.•Listanalchem is a tool that tests models that pretend to explain the origin of biological homochirality, helps find errors, and aids in designing new models.

Stoichiometric network analysis in reaction networks yielding spontaneous mirror symmetry breaking in a prebiotic atmosphere.

The generation of amino acid homochirality under prebiotic atmosphere conditions is a relevant issue in the study of the origin of life. This research is based on the production of amino acids via Strecker synthesis and how it is adjusted to the Kondepudi-Nelson autocatalytic model. The spontaneous mirror symmetry breaking (SMSB) of the new Kondepudi-Nelson-Strecker model, subject to two modifications (with Limited Enantioselective and Cross Inhibition), and also their combination were studied using the stoichiometric network analysis (SNA). In the calculations, the values obtained from the literature for alanine were considered. A total production of alanine of 7.56 × 109 mol year-1 was determined under prebiotic atmosphere conditions and starting from that value, the reaction rates for the models studied were estimated. Only the model with cross inhibition or achiral dimer formation is driven by stochastic fluctuations during SMSB. The stochastic fluctuation was estimated for a value of 2.619 × 10-15 mol L-1. This perturbation was sufficient to trigger SMSB. Finally, the results of SMSB were used to calculate the entropy production for the cross inhibition model.

Implementation of the Theoretical Coulometric Titration Curve in the Determination of the Amount of Substance of Potassium Hydrogen Phthalate: the Search for a Better Metrological Approach.

In metrology, the certification of potassium hydrogen phthalate (KHP) as a reference material is made using the potential primary method of coulometric titration. Usually, this titration is performed in three steps at constant current, where two endpoint (EP) times are determined from the nonlinear regression that fits the empirical W-function (eWf) to the experimental data. As an alternative, we propose the implementation of the theoretical coulometric titration curve (TC). The TC allowed us to compute the KHP amount of substance, the influence of CO2 in the system, the acid dissociation constants for carbonic and phthalic acids, assuming that those species are the only acids present during titration, and the EP times. The amount of substance of KHP estimated with the EP time and obtained from the TC was compared with the results of the eWf, and no statistical difference was found, while the amount of substance, when estimated directly as a parameter of the nonlinear regression of the TC, was lower. Therefore, the traditional method finds the total acidity of the dissolution, and our method finds the KHP purity. In addition, the acid dissociation constants for H2CO3 and phthalic acid estimated in this work agreed with the data reported in the literature. Finally, the description of the coulometric system using the theoretical TC has a solid and well-known chemical support that is not present in the eWf; this fact is essential for the uncertainty budget and the scientific support for coulometry as a potential primary method.

Biological homochirality and stoichiometric network analysis: Variations on Frank's model / Homoquiralidad biológica y el análisis de redes estequiométricas: el modelo de Frank y sus variantes / Homoquiralidade biológica e análise de redes estequiométricas: O modelo de Frank e as suas variantes

Abstract Biological homochirality is modelled using chemical reaction mechanisms that include autocatalytic and inhibition reactions as well as input and output flows. From the mathematical point of view, the differential equations associated with those mechanisms have to exhibit bistability. The search for those bifurcations can be carried out using stoichiometric network analysis. This algorithm simplifies the mathematical analysis and can be implemented in a computer programme, which can help us to analyse chemical networks. However, regardless of the reduction to linear polynomials, which is made possible by this algorithm, in some cases, the complexity and length of the polynomials involved make the analysis unfeasible. This problem has been partially solved by extending the stoichiometric matrix with rows that code the duality relations between the different reactions occurring in the network given as input. All these facts allow us to analyse 28 different network models, highlighting the basic requirements needed by a chemical mechanism to have spontaneous mirror symmetry breaking.

Resumen El origen de la homoquiralidad biológica se ha modelado usando mecanismos de reacción con pasos autocatalíticos, de inhibición y flujos de entrada y salida. Desde el punto de vista de las matemáticas, las ecuaciones diferenciales asociadas a tales mecanismos deben exhibir biestabilidad. La búsqueda de tales bifurcaciones se puede hacer usando el análisis de redes estequiométricas. Tal algoritmo facilita el trabajo matemático y se puede implementar en un programa de computadora, con lo que se simplifica el análisis y ayuda a entender y mejorar los mecanismos de reacción. No obstante, y a pesar de la reducción en la complejidad que es alcanzada usando el análisis de redes estequiométricas, la dificultad y la longitud de los polinomios involucrados hacen que, en los casos más difíciles y de mayor envergadura, la solución de estos no sea posible. En este trabajo se ha superado parcialmente el problema, adicionando a la matriz estequiométrica un conjunto de filas que codifican la relación de dualidad entre las diferentes reacciones presentes en la red química dada como entrada al programa. Así, hemos logrado analizar 28 modelos diferentes de homoquiralidad biológica, extrayendo de ellos el conjunto de requisitos necesarios para tener un modelo cinética y termodinámicamente consistente.

Resumo A origem da homoquiralidade biológica foi modelada usando mecanismos de reação com etapas autocatalíticas, de inibição e fluxos de entrada e saída. Do ponto de vista da matemática, as equações diferenciais associadas a tais mecanismos devem ser instáveis. A instabilidade pode ser estudada usando o algoritmo de análise de redes estequiométricas. Tal algoritmo facilita o trabalho matemático e pode ser implementado num programa de computador, o que simplifica a análise e ajuda a entender e melhorar os mecanismos de reação. No entanto, e apesar da redução na complexidade que é alcançada usando a análise de redes estequiométricas, a complexidade e comprimento dos polinômios envolvidos fazem que, nos casos mais complexos e de maior envergadura, a solução dos mesmos não seja possível. Neste trabalho, o problema foi superado, parcialmente, adicionando à matriz estequiométrica um conjunto de linhas que codificam a relação de dualidade entre as diferentes reações presentes na rede química dada como entrada ao programa. Desta forma foi possível analisar 28 modelos diferentes de homoquiralidade biológica, extraindo deles o conjunto de requisitos necessários para ter um modelo cinético e termodinamicamente consistente.

CHEMical KINetics SimuLATOR (Chemkinlator): A friendly user interface for chemical kinetics simulations / CHEMical KINetics SimuLATOR (Chemkinlator): Una herramienta amigable para realizar simulaciones de cinética química / CHEMical KINetics SimuLATOR (Chemkinlator): Uma ferramenta amigável para realizar simulações de cinética química

Abstract CHEMicalKINetics SimuLATOR (Chemkinlator) is a Graphical User Interface for the simulation of reaction mechanisms. The interface allows the user to see and change the parameters of a reaction network within a single window. Chemkinlator comes with built-in support for three types of kinetic simulations: Time Series, which computes the concentration of all species in an interval of time for the defined model; Bifurcation diagrams, which are the result of running several Time Series simulations over gradually different kinetic rate constants; and Flow/Temperature time series, which takes into account the effect of flow in the Continuous-flow well-Stirred Tank Reactor, and the effect of temperature on the rates constants according to the Arrhenius equation. In our research group, Chemkinlator has been the primary tool used to test the predictions made by algorithms that analyze homochirality phenomena. Chemkinlator is written in C++14 and Qt, and it uses the Fortran subroutine DLSODE to solve the differential equations associated with the reaction networks. Chemkinlator is open source software under the Apache 2.0 license and can be downloaded freely from https://gitlab.com/homochirality/chemkinlator.

Resumen CHEMical KINetics SimuLATOR (Chemkinlator) es una interfaz gráfica para realizar simulaciones de mecanismos de reacción. La interfaz le permite al usuario ver y cambiar los parámetros de una red de reacciones en una única ventana. Chemkinlator puede realizar tres tipos de simulaciones cinéticas: Time Series, calcula la concentración de cada especie en un intervalo de tiempo del modelo estudiado; Bifurcation, es el resultado de ejecutar varias veces las simulaciones del modo Time Series, cambiando gradualmente diferentes constantes de velocidad; y Flow/ Temperature es una serie de tiempo en la que se tiene en cuenta el efecto del flujo considerando un Reactor de Flujo Continuo bien Agitado y el efecto de la temperatura sobre las constantes de velocidad según la ecuación de Arrhenius. En nuestro grupo de investigación, Chemkinlator ha sido la herramienta principal para verificar las predicciones hechas por los algoritmos que analizan el fenómeno de homochiralidad. Chemkinlator está escrito en C++14 y Qt, y usa la subrutina de Fortran DLSODE para resolver las ecuaciones diferenciales relacionadas con los mecanismos de reacción. Chemkinlator es software de código abierto bajo la licencia Apache 2.0 y se puede descargar libremente de https://gitlab.com/homochirality/chemkinlator.

Resumo O CHEMical KINetics SimuLATOR (Chemkinlator) é uma interface gráfica para realizar simulações de mecanismos de reação. A interface permite ao usuário visualizar e alterar os parâmetros de uma rede de reação em uma única janela. O Chemkinlator pode realizar três tipos de simulações cinéticas: Time Series, calcula a concentração de cada espécie em um intervalo de tempo do modelo estudado; Bifurcation, é o resultado de executar várias vezes as simulações do modo Time Series, modificando gradualmente diferentes constantes de velocidade; e Flow/Temperature é uma serie de tempo que se considera o efeito do fluxo considerando um Reator de Fluxo Continuo bem Agitado e o efeito da temperatura sobre as constantes de velocidade pela equação de Arrhenius. No nosso grupo de investigação, o Chemkinlator tem sido a principal ferramenta para verificar as predições realizadas pelos algoritmos que analisam o fenómeno de homoquiralidade. O Chemkinlator está escrito em C++14 e Qt, e usa a sub-rotina de Fortran DLSODE para resolver as equações diferenciais relacionadas com os mecanismos de reação. O Chemkinlator é um software de código aberto baixo a licença Apache 2.0 e pode ser descarregado livremente em https://gitlab.com/homochirality/chemkinlator.

Computing the Parameter Values for the Emergence of Homochirality in Complex Networks.

The goal of our research is the development of algorithmic tools for the analysis of chemical reaction networks proposed as models of biological homochirality. We focus on two algorithmic problems: detecting whether or not a chemical mechanism admits mirror symmetry-breaking; and, given one of those networks as input, sampling the set of racemic steady states that can produce mirror symmetry-breaking. Algorithmic solutions to those two problems will allow us to compute the parameter values for the emergence of homochirality. We found a mathematical criterion for the occurrence of mirror symmetry-breaking. This criterion allows us to compute semialgebraic definitions of the sets of racemic steady states that produce homochirality. Although those semialgebraic definitions can be processed algorithmically, the algorithmic analysis of them becomes unfeasible in most cases, given the nonlinear character of those definitions. We use Clarke's system of convex coordinates to linearize, as much as possible, those semialgebraic definitions. As a result of this work, we get an efficient algorithm that solves both algorithmic problems for networks containing only one enantiomeric pair and a heuristic algorithm that can be used in the general case, with two or more enantiomeric pairs.

THERMOKINETIC STUDY OF THE ZERO, FIRST AND SECOND ORDER REACTIONS IN A PSEUDO-ADIABATIC CALORIMETER: Numerical approach and experimental data / ESTUDIO TERMOCINÉTICO DE LAS REACCIONES DE ORDEN CERO, UNO Y DOS EN UN CALORÍMETRO PSEUDO-ADIABÁTICO: Aproximación numérica y datos experimentales / ESTUDO TERMOCINÉTICO DAS REAÇÕES DE ORDEM ZERO, UM E DOIS NUM CALORÍMETRO PSEUDOADIABÁTICO: aproximação numérica e dados experimentais

The signal produced by a pseudo-adiaba-tic calorimeter is simulated by numerical solution of the differential equations that model the chemical kinetics [1], the ther-mal properties of the calorimetric cell [2], and the response of the thermistor used as a thermometric sensor [3]. (to see formula math access full text) These equations show that the calorimetric signal is related with concentration in a complex way. Therefore, a compa-rison between the signáis of the three basic kinetics reactions (zero, first and second order) was made, as a first step to obtain a standard procedure to follow chemical kinetics using a calorimeter. In order to help understanding this relation-ship, the initial rate method was applied to the simulated data to assess the rela-tionship between the order and the kine-tic constants calculated with those used for the simulations. As it was expected, the initial rate method for the calorime-tric data, do not give a slope directly re-lated with the order of the reaction, as it would be produced, for example, in data from a spectrophotometer. However, a linear relationship was found between what we call the "calorimetric order" and the kinetic order. Finally, the deve-loped procedure was applied to the stu-dy of the H2O2 decomposition catalyzed with Fe3+ in homogeneous phase and with activated carbon in heterogeneous phase, fnding the order and the kinetics constants of the global processes, which were in close agreement with those in the literature.

La señal producida por un calorímetro pseudo-adiabático se simuló mediante la solución numérica de las ecuaciones diferenciales que modelan la cinética química [1], las propiedades térmicas de la celda calorimétrica [2] y la respuesta del termistor que se usó como sensor termométrico [3]. (vea texto completo) Los resultados obtenidos de las simulaciones se usaron para hacer una comparación entre las señales de las tres cinéticas básicas (orden cero, uno y dos). Esto sirvió para establecer un protocolo de estudio de la cinética de una reacción a partir de medidas calorimétricas, lo cual resulta fundamental, ya que, como se ve en las ecuaciones anteriores, la relación entre el orden de reacción y la señal calorimétrica no es sencilla. Para esclarecer este punto, se realizó el estudio de las señales calorimétricas simuladas, empleando el método de las velocidades iniciales, y se compararon los resultados así obtenidos (orden de reacción y constante cinética) con los valores usados para las simulaciones. Como era de esperarse, los "órdenes de reacción calorimétricos" no coincidieron con los órdenes cinéticos usados en las simulaciones, como sí sucede, por ejemplo, en el caso de datos espectrofotométricos. Sin embargo, se pudo establecer una relación lineal entre el "orden calorimétrico" y el orden cinético que permite obtener el orden de reacción de un proceso que se estudia con un calorímetro. Finalmente, el procedimiento desarrollado se aplicó a los resultados calorimétricos experimentales de la descomposición del H2O2 catalizada en fase homogénea con Fe3+ y en fase heterogénea con carbón activado, encontrando los órdenes de reacción y las constantes cinéticas respectivas de cada proceso global, los cuales presentaron buena coincidencia con los valores reportados en la literatura.

O sinal produzido por um calorímetro pseudoadiabático foi simulado mediante a solução numérica das equações dife-renciais que modelam a cinética química [1], as propriedades térmicas da célula calorimétrica [2] e da resposta do termis-tor que foi usado como sensor termométrico [3]. (Acesse texto completo para fórmula) Os resultados obtidos das simulações foram usados para realizar urna compa-ração entre os sinais das três cinéticas básicas (ordem zero, um e dois). Isso serviu para estabelecer um protocolo de estudo da cinética de uma reação a partir de medidas calorimétricas, o qual resulta fundamental, já que como se vê nas equações anteriores, a relação entre a ordem de reação e o sinal calorimétrico não é simples. Para esclarecer este ponto, foi realizado o estudo dos sinais calorimétricos simulados usando o método das velocidades iniciais e compa-raram-se os resultados assim obtidos (ordem de reação e constante cinética) com os valores usados para as simulações. Como era de esperar, as ordens de reação "calorimétricas" não coincidiram com as ordens cinéticas usadas nas simulações, como sucede no caso de dados espectrofotométricos. No entanto, foi possível estabelecer uma relac" o linear entre a ordem "calorimétrica e a ordem cinética que permite obter a ordem de reação de um processo que se estuda com um calorímetro. Finalmente, o procedimento desenvolvido foi aplicado aos resultados calorimétricos experimentais da decomposição de H2O2 catalisada em fase homogênea com Fe3+ e em fase heterogênea com carvão ativado, encontrando as ordens de reação e as constantes cinéticas respectivas de cada processo global, os quais apresentaram boa coincidência com os valores reportados na literatura.

DESARROLLO DE MÉTODOS DE ANÁLISIS POR INYECCIÓN EN FLUJO A PARTIR DE PROCEDIMIENTOS CLÁSICOS: Determinación de Pb en agua / DEVELOPMENT OF FLOW INJECTION ANALYSIS METHODS BY CLASSICAL PROCEDURES: Determination of Pb in water / DESENVOLVIMENTO DE MÉTODOS DE ANÁLISE POR INJEÇÃO EM FLUXO A PARTIR DE PROCEDIMENTOS CLÁSSICOS: determinação de Pb em água

El análisis químico día a día se acerca más a la automatización, buscando satisfacer las necesidades actuales de resultados rápidos y confiables. Los sistemas de análisis en flujo (FIA - Flow Injection Analysis) son una de las formas de aproximarse a la automatización. En este artículo se presentan los pasos necesarios para implementar una metodología FIA, para la determinación de Pb(II) en agua, partiendo de la revisión de los procedimientos clásicos y describiendo detalladamente los pasos necesarios para implementar la técnica de análisis en flujo. El trabajo produjo un método de análisis de Pb en agua que usa ditizona disuelta en isopropanol (agente cromogénico), en presencia de bromuro de cetiltrimetil amonio (CTAB), para solubilizar en agua el complejo, cuyas características más sobresalientes fueron: volumen de inyección de muestra de 81,7 µL, velocidad de flujo de 8,0 mL/min, tiempo de toma de espectros 1,4 s e intervalo lineal de 1,0 a 40 mg L-1.

Chemical analysis has evolved towards automation to satisfy the current requirements: fast analysis and certainty in the results. Flow injection analysis (FIA) is a way to reach automation. This work presents the necessary steps to obtain an optimized FIA methodology for the determination of Pb(II) in water by classic methods. The result was a FIA method to determinate Pb with dithizone (chromogenic agent) dissolved in iso-propyl alcohol, using cethyltrimethylammonium bromide (CTAB) to solubilize the complex. The main characteristics of the method were: injection sample volume 81.7 µL, flow 8.0 mL/min, spectra acquisition time 1.4 s and linear range 1 to 40 mg L-1.

Cada dia, a análise química é mais cerca da automatização com o fim de satisfazer as necessidades atuais de resultados rápidos e confiáveis. Os sistemas de análise em fluxo (FIA - Flow Inyection Analysis) são uma das formas de aproximação à automatização. Este artigo apresenta os passos necessários para implementar uma metodologia FIA para a determinação de Pb(II) em água, partindo da revisão dos procedimentos clássicos e descrevendo detalhadamente os passos necessários para implementar a técnica de análise em fluxo. Os resultado são um método de análise de Pb em água que usa ditizona dissolvida em isopropanol (agente cromogénico) na presença de bromuro de cetiltrimetil amônio (CTAB), usado para solubilizar o complexo em água. As características principais do método foram: volume de injeção de amostra de 81,7 µL, velocidade de fluxo de 8,0 mL min-1, tempo de aquisição de espectros de 1,4 s e intervalo linear de 0.9 a 40 mg L-1.

Photophysics and photochemistry of 1-nitropyrene.

1-Nitropyrene (1NPy) is the most abundant nitropolycyclic aromatic contaminant encountered in diesel exhausts. Understanding its photochemistry is important because of its carcinogenic and mutagenic properties, and potential phototransformations into biologically active products. We have studied the photophysics and photochemistry of 1NPy in solvents that could mimic the microenvironments in which it can be found in the atmospheric aerosol, using nanosecond laser flash photolysis, and conventional absorption and fluorescence techniques. Significant interactions between 1NPy and solvent molecules are demonstrated from the changes in the magnitude of the molar absorption coefficient, bandwidth at half-peak, oscillator strengths, absorption maxima, Stokes shifts, and fluorescence yield. The latter are very low (10 (-4)), increasing slightly with solvent polarity. Low temperature phosphorescence and room temperature transient absorption spectra demonstrate the presence of a low energy (3)(pi,pi*) triplet state, which decays with rate constants on the order of 10 (4)-10 (5) s (-1). This state is effectively quenched by known triplet quenchers at diffusion control rates. Intersystem crossing yields of 0.40-0.60 were determined. A long-lived absorption, which grows within the laser pulse, and simultaneously with the triplet state, presents a maximum absorption in the wavelength region of 420-440 nm. Its initial yield and lifetime depend on the solvent polarity. This species is assigned to the pyrenoxy radical that decays following a pseudo-first-order process by abstracting a hydrogen atom from the solvent to form one the major photoproducts, 1-hydroxypyrene. The (3)(pi,pi*) state reacts readily ( k approximately 10 (7)-10 (9) M (-1) s (-1)) with substances with hydrogen donor abilities encountered in the aerosol, forming a protonated radical that presents an absorption band with maximum at 420 nm.